Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:15 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the contiBAIT package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/contiBAIT.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 393/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
contiBAIT 1.23.1 (landing page) Kieran O'Neill
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: contiBAIT |
Version: 1.23.1 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:contiBAIT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings contiBAIT_1.23.1.tar.gz |
StartedAt: 2022-03-17 18:48:12 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 18:53:01 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 288.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: contiBAIT.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:contiBAIT.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings contiBAIT_1.23.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'contiBAIT/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'contiBAIT' version '1.23.1' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'contiBAIT' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT' See 'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: extdata 3.4Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ideogramPlot.func: no visible binding for global variable 'w' ideogramPlot.func: no visible binding for global variable 'w2' makeChrTable: no visible global function definition for 'queryHits' makeChrTable: no visible global function definition for 'subjectHits' orderContigsGreedy: no visible global function definition for 'makeCluster' orderContigsGreedy: no visible global function definition for 'clusterCall' orderContigsGreedy: no visible global function definition for 'stopCluster' strandSeqFreqTable: no visible global function definition for 'queryHits' strandSeqFreqTable: no visible global function definition for 'subjectHits' ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible binding for global variable 'w' ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible binding for global variable 'w2' Undefined global functions or variables: clusterCall makeCluster queryHits stopCluster subjectHits w w2 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method': '...' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'D:/biocbuild/bbs-3.15-bioc/R/library/contiBAIT/libs/x64/contiBAIT.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/contiBAIT.Rcheck/00check.log' for details.
contiBAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL contiBAIT ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'contiBAIT' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c buildLinkageGroups.cpp -o buildLinkageGroups.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c computeSim.cpp -o computeSim.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c orderContigsGreedy.cpp -o orderContigsGreedy.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT' ** help *** installing help indices converting help for package 'contiBAIT' finding HTML links ... done BAIT html ChrTable html ContigOrdering html LibraryGroupList html LinkageGroupList html StrandFreqMatrix html StrandReadMatrix html StrandStateList html StrandStateMatrix html barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method html clusterContigs-StrandStateMatrix-method html contiBAIT html exampleChrTable html exampleContigOrder html exampleCrickFreq html exampleDividedChr html exampleLGList html exampleLibList html exampleReadCounts html exampleStrandFreq html exampleWCMatrix html exampleWatsonFreq html findSexGroups-LinkageGroupList-StrandStateMatrix-method html findSimilarLibraries html fixLinkageGroups html flipOrderedLinkageGroups html highlightAssemblyErrors html ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method html locateMisorients html makeBoxPlot html makeChrTable html mapGapFromOverlap html mergeFlankedLGs html orderAllLinkageGroups html orderContigsGreedy html orderContigsTSP html plotContigOrder html plotLGDistances-LinkageGroupList-StrandStateMatrix-method html plotWCdistribution-StrandFreqMatrix-method html preprocessStrandTable-StrandFreqMatrix-method html reorientAndMergeLGs html show-ContigOrdering-method html show-LibraryGroupList-method html show-LinkageGroupList-method html show-OrientationFrame-method html show-StrandFreqMatrix-method html show-StrandReadMatrix-method html show-StrandStateList-method html show-StrandStateMatrix-method html strandSeqFreqTable html thoroughBed html writeBed html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT' ** testing if installed package can be loaded from final location Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT' ** testing if installed package keeps a record of temporary installation path * DONE (contiBAIT) Making 'packages.html' ... done
contiBAIT.Rcheck/contiBAIT-Ex.timings
name | user | system | elapsed | |
BAIT | 0 | 0 | 0 | |
ContigOrdering | 0 | 0 | 0 | |
LibraryGroupList | 0 | 0 | 0 | |
LinkageGroupList | 0 | 0 | 0 | |
StrandFreqMatrix | 0.02 | 0.00 | 0.01 | |
StrandReadMatrix | 0.00 | 0.02 | 0.02 | |
StrandStateMatrix | 0 | 0 | 0 | |
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.34 | 0.01 | 0.36 | |
clusterContigs-StrandStateMatrix-method | 0.02 | 0.00 | 0.01 | |
contiBAIT | 3.52 | 0.52 | 4.03 | |
findSimilarLibraries | 0.35 | 0.02 | 0.38 | |
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 1.54 | 0.04 | 1.58 | |
makeBoxPlot | 0.04 | 0.00 | 0.04 | |
makeChrTable | 0.63 | 0.00 | 0.63 | |
orderAllLinkageGroups | 1.04 | 0.08 | 1.12 | |
plotContigOrder | 0.21 | 0.00 | 0.21 | |
plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.08 | 0.00 | 0.08 | |
plotWCdistribution-StrandFreqMatrix-method | 0.04 | 0.00 | 0.05 | |
preprocessStrandTable-StrandFreqMatrix-method | 0.14 | 0.00 | 0.14 | |
reorientAndMergeLGs | 0.07 | 0.00 | 0.06 | |
strandSeqFreqTable | 2.61 | 0.04 | 2.66 | |
thoroughBed | 0.01 | 0.02 | 0.03 | |
writeBed | 0 | 0 | 0 | |